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Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.

copied from cf-post-staging / r-ape
Type Size Name Uploaded Downloads Labels
conda 2.1 MB | linux-64/r-ape-5.1-r351h29659fb_1002.tar.bz2  6 years and 11 months ago 6258 main gcc7 cf202003
conda 2.2 MB | win-64/r-ape-5.1-r351h6115d3f_1002.tar.bz2  6 years and 11 months ago 1735 main cf202003 cf201901
conda 2.1 MB | osx-64/r-ape-5.1-r351h466af19_1002.tar.bz2  6 years and 11 months ago 557 main gcc7 cf202003
conda 2.2 MB | win-64/r-ape-5.1-r351h6115d3f_2.tar.bz2  7 years and 1 month ago 1761 main cf202003 cf201901
conda 1.6 MB | win-64/r-ape-5.1-r341h6115d3f_2.tar.bz2  7 years and 1 month ago 1765 main cf202003 cf201901
conda 2.1 MB | osx-64/r-ape-5.1-r351h9d2a408_2.tar.bz2  7 years and 1 month ago 628 main cf202003 cf201901
conda 2.2 MB | linux-64/r-ape-5.1-r351h9d2a408_2.tar.bz2  7 years and 1 month ago 6597 main cf202003 cf201901
conda 1.5 MB | linux-64/r-ape-5.1-r341h9d2a408_2.tar.bz2  7 years and 1 month ago 7602 main cf202003 cf201901
conda 1.5 MB | osx-64/r-ape-5.1-r341h9d2a408_2.tar.bz2  7 years and 1 month ago 595 main cf202003 cf201901
conda 1.6 MB | win-64/r-ape-5.1-r341hca4a3dc_1.tar.bz2  7 years and 2 months ago 1796 main cf202003 cf201901
conda 1.5 MB | osx-64/r-ape-5.1-r341hfc679d8_1.tar.bz2  7 years and 2 months ago 418 main cf202003 cf201901
conda 1.5 MB | linux-64/r-ape-5.1-r341hfc679d8_1.tar.bz2  7 years and 2 months ago 5518 main cf202003 cf201901
conda 1.6 MB | win-64/r-ape-5.1-r3.3.2_0.tar.bz2  7 years and 6 months ago 2926 main cf202003 cf201901
conda 1.6 MB | win-64/r-ape-5.1-r3.4.1_0.tar.bz2  7 years and 6 months ago 2956 main cf202003 cf201901
conda 1.5 MB | osx-64/r-ape-5.1-r3.4.1_0.tar.bz2  7 years and 6 months ago 1720 main cf202003 cf201901
conda 1.5 MB | osx-64/r-ape-5.1-r3.3.2_0.tar.bz2  7 years and 6 months ago 1590 main cf202003 cf201901
conda 1.5 MB | linux-64/r-ape-5.1-r3.4.1_0.tar.bz2  7 years and 6 months ago 3246 main cf202003 cf201901
conda 1.5 MB | linux-64/r-ape-5.1-r3.3.2_0.tar.bz2  7 years and 6 months ago 8338 main cf202003 cf201901

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